[BioC] RMA error in cdf environment with removed probes (Yeast2)
drnevich at illinois.edu
Wed Dec 17 16:04:25 CET 2008
I'm assuming that the RemoveProbes.r function is the one I have
posted to the Bioconductor mailing list several times, mostly
recently with some changes on Sept 24, 2008?
If so, would you post your entire session, including the code you
used to remove the probe sets and probes, along with your
sessionInfo()? That should give us more details so we can help you.
At 10:08 PM 12/16/2008, Omri Yahel wrote:
>I am encountering an error during RMA of an affybatch.
>I have used RemoveProbes.r to remove all S. pombe probesets and 864
>individual S.cerevisiae probes from the yeast2 platform.
> > data
>size of arrays=496x496 features (11 kb)
>cdf=Yeast_2 (5900 affyids)
>number of samples=26
>number of genes=5900
> > length(pm(data[,1]))
>When I attempt to compute the eset
> > eset <- rma(data)
>Error in rma(data) : length of 'dimnames'  not equal to array extent
>I assume this has something to do with the removal of individual probes from
>the environment, but am not sure and do not know how to remedy this.
>Any help appreciated
>School of Biological Sciences
>University of Auckland, New Zealand
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>Bioconductor at stat.math.ethz.ch
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Jenny Drnevich, Ph.D.
Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign
1201 W. Gregory Dr.
Urbana, IL 61801
e-mail: drnevich at illinois.edu
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